#StackBounty: #python #machine-learning #deep-learning Remove white borders from segmented images

Bounty: 50

I’m new to image processing and am trying to segment lung CT images using Kmeans by using code below:

def process_mask(mask):
    convex_mask = np.copy(mask)
    for i_layer in range(convex_mask.shape[0]):
        mask1  = np.ascontiguousarray(mask[i_layer])
        if np.sum(mask1)>0:
            mask2 = convex_hull_image(mask1)
            if np.sum(mask2)>2*np.sum(mask1):
                mask2 = mask1
        else:
            mask2 = mask1
        convex_mask[i_layer] = mask2
    struct = generate_binary_structure(3,1)
    dilatedMask = binary_dilation(convex_mask,structure=struct,iterations=10)

    return dilatedMask

def lumTrans(img):
    lungwin = np.array([-1200.,600.])
    newimg = (img-lungwin[0])/(lungwin[1]-lungwin[0])
    newimg[newimg<0]=0
    newimg[newimg>1]=1
    newimg = (newimg*255).astype('uint8')
    return newimg


def lungSeg(imgs_to_process,output,name):

    if os.path.exists(output+'/'+name+'_clean.npy') : return
    imgs_to_process = Image.open(imgs_to_process)
    
    img_to_save = imgs_to_process.copy()
    img_to_save = np.asarray(img_to_save).astype('uint8')

    imgs_to_process = lumTrans(imgs_to_process)    
    imgs_to_process = np.expand_dims(imgs_to_process, axis=0)
    x,y,z = imgs_to_process.shape 
  
    img_array = imgs_to_process.copy()  
    A1 = int(y/(512./100))
    A2 = int(y/(512./400))

    A3 = int(y/(512./475))
    A4 = int(y/(512./40))
    A5 = int(y/(512./470))
    for i in range(len(imgs_to_process)):
        img = imgs_to_process[i]
        print(img.shape)
        x,y = img.shape
        #Standardize the pixel values
        allmean = np.mean(img)
        allstd = np.std(img)
        img = img-allmean
        img = img/allstd
        # Find the average pixel value near the lungs
        # to renormalize washed out images
        middle = img[A1:A2,A1:A2] 
        mean = np.mean(middle)  
        max = np.max(img)
        min = np.min(img)
        
        kmeans = KMeans(n_clusters=2).fit(np.reshape(middle,[np.prod(middle.shape),1]))
        centers = sorted(kmeans.cluster_centers_.flatten())
        threshold = np.mean(centers)
        thresh_img = np.where(img<threshold,1.0,0.0)  # threshold the image
       
        eroded = morphology.erosion(thresh_img,np.ones([4,4]))
        dilation = morphology.dilation(eroded,np.ones([10,10]))
        
        labels = measure.label(dilation)
        label_vals = np.unique(labels)
        regions = measure.regionprops(labels)
        good_labels = []
        for prop in regions:
            B = prop.bbox
            if B[2]-B[0]<A3 and B[3]-B[1]<A3 and B[0]>A4 and B[2]<A5:
                good_labels.append(prop.label)
        mask = np.ndarray([x,y],dtype=np.int8)
        mask[:] = 0
       
        for N in good_labels:
            mask = mask + np.where(labels==N,1,0)
        mask = morphology.dilation(mask,np.ones([10,10])) # one last dilation
        imgs_to_process[i] = mask

    m1 = imgs_to_process
    
    convex_mask = m1
    dm1 = process_mask(m1)
    dilatedMask = dm1
    Mask = m1
    extramask = dilatedMask ^ Mask
    bone_thresh = 180
    pad_value = 0

    img_array[np.isnan(img_array)]=-2000
    sliceim = img_array
    sliceim = sliceim*dilatedMask+pad_value*(1-dilatedMask).astype('uint8')
    bones = sliceim*extramask>bone_thresh
    sliceim[bones] = pad_value


    x,y,z = sliceim.shape
    if not os.path.exists(output): 
        os.makedirs(output)
    
    img_to_save[sliceim.squeeze()==0] = 0
    
    im = Image.fromarray(img_to_save)

    im.save(output + name + '.png', 'PNG')

The problem is the segmented lung still contains white borderers like this:

segmented lung (output):

segmented lung

unsegmented lung (input):

unsegmented lung

The full code can be found in Google Colab Notebook. code.

And sample of the dataset is here.


Get this bounty!!!

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